1983 research outputs found
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A Novel Dual NK Cell CAR Targeting CTLA-4 to Induce Regulatory T Cell Depletion in Head and Neck Cancer Microenvironment
No full textHead and neck cancer (HNC) is one of the most common cancers in the US affecting 66,470 people in 2022. Despite advances in chemotherapy, radiation therapy, and surgery, about 50% of patients still develop recurrent/metastatic disease (R/M) with a median survival of 12 months. The immune system plays a key role in the development of HNC. Epidermal growth factor receptor (EGFR) is overexpressed in approximately 80-90% of HNC cells. Subsequently, many studies use cetuximab, a known anti-EGFR antibody, to target HNC, but success has been limited. One of the major mechanisms of immune escape in solid tumors including HNC is via cytotoxic T lymphocyte-associated protein 4 (CTLA-4). Evidence has shown that intratumoral CD4+CD25+Foxp3+ regulatory T cells (Tregs) expressing CTLA-4 suppress NK cell cytotoxicity and contribute to the progression of HNC. With recent advances, immunotherapy has become a promising and potentially less toxic treatment option for HNC and other cancers. However, no studies have successfully eliminated the immunosuppressive Tregs associated with HNC. To address this major hurdle, my project aims to deplete Tregs in the HNC tumor microenvironment (TME) with a novel dual NK cell CAR against EGFR as the primary chimeric antigen receptor and secondary arming with single chain variable fragment (scFv) against CTLA-4. Our EGFR-targeting CAR was successfully expressed on both NK-92 and primary CIML NK cells and led to enhanced target cell killing in vitro. We also successfully transduced Jurkat cells with our designed CTLA-4-targeting CAR. Future efforts will focus on testing the cytotoxicity of CTLA-4-targeting CAR NK cells. We will then concentrate on constructing dual NK cell CAR and testing the functions of our dual CAR in pre-clinical models
Household energy demand in Urban China: Accounting for regional prices and rapid income change
No full textUnderstanding the rapidly rising demand for energy in China is essential to efforts to reduce the country’s energy use and environmental damage. In response to rising incomes and changing prices and demographics, household use of various fuels, electricity and gasoline has changed dramatically in China. In this paper, we estimate both income and price elasticities for various energy types using Chinese urban household micro-data collected by National bureau of Statistics, by applying a two-stage budgeting AIDS model. We find that total energy is price and income inelastic for all income groups after accounting for demographic and regional effects. Our estimated electricity price elasticity ranges from -0.49 to -0.57, gas price elasticity ranges from -0.46 to -0.94, and gasoline price elasticity ranges from -0.85 to -0.94. Income elasticity for various energy types range from 0.57 to 0.94. Demand for coal is most price and income elastic among the poor, whereas gasoline demand is elastic for the rich.Engineering and Applied SciencesAccepted Manuscrip
Effects of Extracellular Matrix Viscoelasticity on Cellular Behaviour
No full textSignificant research over the past two decades has established that extracellular matrix (ECM) elasticity, or stiffness, impacts fundamental cell processes including spreading, growth, proliferation, migration, differentiation, and organoid formation. Linearly elastic polyacrylamide hydrogels and polydimethylsiloxane (PDMS) elastomers coated with ECM proteins have become widely-used tools for assessing the role of stiffness, and results from these experiments are often assumed to closely reproduce the effect of the mechanical environment experienced by cells in vivo. However, tissues and ECMs are not linearly elastic materials – they in fact exhibit far more complex mechanical behaviors, including viscoelasticity, or a time-dependent response to loading or deformation, as well as mechanical plasticity and nonlinear elasticity. Recent work has revealed that matrix viscoelasticity regulates these same fundamental cell processes, and importantly can promote behaviors not observed with elastic hydrogels in both 2D and 3D culture microenvironments. These important findings have provided new insights into cell-matrix interactions and have given context as to how these interactions differentially modulate mechano-sensitive molecular pathways in cells. Moreover, these results indicate new design guidelines for the next generation of biomaterials that better match tissue and ECM mechanics for in vitro tissue models and applications in regenerative medicine.Accepted Manuscrip
An atlas of healthy and injured cell states and niches in the human kidney
No full textUnderstanding kidney disease relies upon defining the complexity of cell types and states, their associated molecular profiles, and interactions within tissue neighborhoods. We applied multiple single-cell or -nucleus assays (>400,000 nuclei/cells) and spatial imaging technologies to a broad spectrum of healthy reference (45 donors) and diseased (48 patients) kidneys. This has provided a high resolution cellular atlas of 51 main cell types that include rare and novel cell populations. The multi-omic approach provides detailed transcriptomic profiles, epigenomic regulatory factors, and spatial localizations spanning the entire kidney. We further define 28 cellular states across nephron segments and interstitium that were altered in kidney injury, encompassing cycling, adaptive or maladaptive repair, transitioning and degenerative states. Molecular signatures permitted localization of these states within injury neighborhoods using spatial transcriptomics, while large-scale 3D imaging analysis (~1.2 million neighborhoods) provided corresponding linkages to active immune responses. These analyses defined biological pathways relevant to injury time-course and niches, including signatures underlying epithelial repair that predicted maladaptive states associated with a decline in kidney function. This integrated multimodal spatial cell atlas of healthy and diseased human kidneys represents the most comprehensive benchmark of cellular states, neighborhoods, outcome-associated signatures, and publicly available interactive visualizations.Version of Recor
Ultra-fast intramolecular singlet fission to persistent multiexcitons by molecular design
No full textSinglet fission—that is, the generation of two triplets from a lone singlet state—has recently resurfaced as a promising process for the generation of multiexcitons in organic systems. Although advances in this area have led to the discovery of modular classes of chromophores, controlling the fate of the multiexciton states has been a major challenge; for example, promoting fast multiexciton generation while maintaining long triplet lifetimes. Unravelling the dynamical evolution of the spin- and energy conversion processes from the transition of singlet excitons to correlated triplet pairs and individual triplet excitons is necessary to design materials that are optimized for translational technologies. Here, we engineer molecules featuring a discrete energy gradient that promotes the migration of strongly coupled triplet pairs to a spatially separated, weakly coupled state that readily dissociates into free triplets. This ’energy cleft’ concept allows us to combine the amplification and migration processes within a single molecule, with rapid dissociation of tightly bound triplet pairs into individual triplets that exhibit lifetimes of ~20 µs.Chemistry and Chemical BiologyVersion of Recor
THE MIDDLE GROUND: Photography and Architectural Preservation in the Era of Social Media
No full textBoth photography and preservation represent a state of the non-present image and try to freeze time and places in their original stage or appearance. The thesis aims to explore the relationship between photography and architecture preservation. A typical block of Shanghai's historic typology- Lilong, is selected as an experiment
Protein folding and misfolding in the cell: towards an atomistic picture
No full textProteins, the molecules that perform the majority of tasks required to sustain life at the molecular level, must generally fold into a specific structure in order to perform their molecular functions. Despite decades of research, we do not fully understand how proteins fold up into their correct structures, starting off as a linear chain of amino acids, while avoiding incorrect misfolded structures linked to diseases such as Alzheimer's, Parkinson's, and various forms of cancer. It was previously believed that most proteins can autonomously fold into their native structures, driven by the physical and chemical interactions between a protein's constituent amino acids. But growing evidence suggests that, for a large number of proteins, these interactions instead cause the chain to misfold into nonnative structures, thus necessitating the assistance of additional cellular mechanisms to ensure the correct native state is attained. For instance, in the cell many proteins can start to fold as they are being synthesized on the ribosome. Previous studies have demonstrated that this process, known as co-translational folding, can significantly improve the native folding efficiency for many proteins that cannot efficiently fold autonomously.
Furthermore, recent bioinformatics studies have shown that, in many organisms, co-translational folding tends to begin at nascent chain lengths associated with evolutionarily conserved, slowly translating codons, suggesting that it is widely beneficial to slow down synthesis and give proteins time to fold co-translationally.
But the precise molecular mechanisms through which co-translational folding helps proteins efficiently reach their native state and avoid detrimental misfolded states, remains poorly understood, largely owing to immense technical difficulties in studying this highly dynamic process. Such an understanding is necessary if we are to rationally manipulate protein quality control mechanisms in the cell to alleviate misfolding diseases.
The goal of this dissertation is to develop and apply novel interdisciplinary pipeline, combining theory, atomistic simulation, and in vitro experiments to elucidate, at the molecular level, why certain proteins which face difficulty folding autonomously can reach their native states much more efficiently via co-translational folding. In Chapter 1, we present a novel algorithm, known as DBFOLD, that uses atomistic Monte-Carlo simulation, machine-learning based analysis, and statistical physics theory to predict detailed folding pathways and rates for large proteins while accounting for the possibility of non-native misfolding--a crucial feature omitted from many existing atomistic simulation algorithms for the sake of computational feasibility. In Chapter 2, we apply the DBFOLD algorithm to predict the co-translational folding mechanisms
of certain E. coli proteins with conserved clusters of slow codons and to explain why these proteins benefit from folding co-translationally. We find that, for these proteins, there is a narrow window of intermediate translation lengths at which native-like folding is both thermodynamically favorable and kinetically fast. But beyond these lengths, folding kinetics slow down by orders of magnitude due to deep nonnative traps stabilized by newly-synthesized C-terminal residues. Thus, co-translational folding is predicted to help these proteins circumvent deep kinetic traps and rapidly reach their native state--strategically-evolved slow codons at these lengths can give the nascent chain additional time to take advantage of these optimal folding windows.
A key advantage of our atomistic simulations is that they generate highly, specific, experimentally testable predictions. In Chapter 3, we test these predictions as they apply to E. coli MarR, one of the proteins predicted to circumvent deep folding traps via co-translational folding. Using in vitro refolding and mutagenesis experiments, we confirm the existence of these trapped states and preliminarily show that the simulations can accurately predict their structure and underlying molecular interactions. Our experiments thus lend support to our atomistic model for the MarR folding landscape, and indirectly support the predicted mechanism by which co-translational folding may allow folding traps to be circumvented. The work also sheds light on evolutionary tradeoffs that MarR faces between various biophysical properties under selection.
Finally in Chapter 4, we apply our combined computational/experimental methodology to investigate the folding mechanism of the receptor binding domain (RBD) of the SARS-CoV-2--the virus behind the Covid-19 pandemic--with the ultimate goal of linking biophysical folding properties to viral fitness and pathology. We find that the RBD can only refold reversibly if its disulfides are kept intact during denaturation, whereas their disruption leads to spontaneous misfolding into a molten-globule like nonnative state which is highly aggregation-prone. But our simulations predict that the RBD can solve this problem by folding co-translationally during secretion in to the endoplasmic reticulum--this process is predicted to increase the odds that the correct disulfides form and ultimately lock the protein into its native state, thus minimizing nonnative misfolding.
Together, these results present and validate a novel interdisciplinary pipeline that significantly advances our detailed molecular understanding of co-translational protein folding in the cell--a process long known to be beneficial albeit through poorly understood mechanisms. We expect that future work will continue probing the detailed molecular models generated here, along with their crucial evolutionary and biomedical implications
Equity for All: Effectively Implementing a Student Support Model While Managing Change
No full textAll students attending public schools should receive the best educational experience no matter their academic, social/emotional and/or physical need. School districts have a responsibility to deliver on the promise of an equitable and excellent education for all students including for those students who require more. Systemic structures, policies and implementation support are required to ensure all students receive what they need and to access learning in the least restrictive educational setting.
Research indicates that use of a Multi-Tiered System of Support (MTSS) framework can support students with diverse learning needs. The framework identifies Student Support Models as a structure necessary to identify students that need additional support. Full implementation of such structures can be complicated due to the challenges of institutional change. As Scott points out: Regulative, Cultural-Cognitive, and Normative forces cause resistance to change within institutions (1994). Schools may be defined as institutions since they are “a relatively stable and legitimated system of interrelated beliefs, values, practices, and structures creating conditions that constrain but also enable particular actions and outcomes…(Bridwell-Mitchell, 2019).” My analysis explores existing challenges caused by these institutional factors and steps the school district can take to overcome them.
As a resident in Revere Public Schools, I conducted an analysis of why the current Student Support Team model and District Curriculum and Accommodation Plan were not working as intended. In this Capstone, I detail how I explored Revere Public School’s intervention process as established through Building Based Support Teams (BBST) and led a stakeholder group in restructuring and improving the intervention system. I will describe how the stakeholder group centered the redesign of systems and tools needed to improve support for learners while navigating institutional forces. This capstone provides an analysis of why two structures, the Student Support Team model and District Curriculum and Accommodation Plan, which were intended to deliver necessary support to students in the Revere Public Schools, were not working as intended. My findings show this is largely due to institutional factors. Additionally, I present opportunities and challenges the district will likely encounter during the change process and strategies to support the examination and advancement of organizational practices in order to better meet student needs
Democracy and the University: America and the Reconstruction of German Higher Education, 1945-1966
No full textThis dissertation explores the intellectual and practical debates over the role of the university in a democratic society by examining the reconstruction and reorientation of German universities in the aftermath of the Second World War, encouraged and led largely by the United States. Drawing on archival materials from universities, foundations, and the US Government, as well as contemporary published sources in journals, conference proceedings, and other forums for discussing the goals of higher education, it traces the efforts made by policy-makers, educators, and philosophers, principally American and German, to develop a system of university education that would safeguard democracy in the so-called “free world,” including West Germany. I argue that a coherent and identifiable doctrine of the role of the university in a democratic society developed in this period. Politically engaged, with equitable and democratic governance, and responsive to civil society, this model of the university attempted not only to respond to the perceived political threats of Fascist authoritarianism and Communism, but also expressed a positive vision of higher education as a source of democratic renewal and a mechanism for producing democratic citizens and leaders. I contribute not only to the literature surrounding the development of higher education in Germany and the postwar process of democratic development there, but also to the general discussion of a model of higher education that dominated the latter half of the twentieth century
ELOF1 Is a Transcription-Coupled DNA Repair Factor That Directs RNA Polymerase II Ubiquitylation
No full textCells employ transcription-coupled repair (TCR) to eliminate transcription-blocking DNA lesions. DNA damage-induced binding of the TCR-specific repair factor CSB to RNA polymerase II (RNAPII) triggers RNAPII ubiquitylation at a single lysine (K1268) by the CRL4CSA ubiquitin ligase. How CRL4CSA is specifically directed toward the K1268 site is unknown. Here, we identify 5 ELOF1 as the missing link that facilitates RNAPII ubiquitylation, a key signal for the assembly of downstream repair factors. This function requires its constitutive interaction with RNAPII close to the K1268 site, revealing ELOF1 as a specificity factor that interacts with and positions CRL4CSA for optimal RNAPII ubiquitylation. Drug-genetic interaction screening also reveals a CSB-independent compensatory pathway in which ELOF1 protects cells against DNA replication stress 10 by preventing DNA damage-induced R-loops. Our study offers key insights into the molecular mechanisms of TCR and provides a genetic framework of the interplay between the transcriptional stress response and DNA replication.Accepted Manuscrip